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学科主题: 计算机化学
题名: Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
其他题名: Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set
作者: LI YAN1; LIU ZHIHAI1; LI JIE1; HAN LI1; LIU JIE1; ZHAO ZHIXIONG1; Wang RX(王任小)1
通讯作者: 王任小
刊名: J. Chem Inf. Model.
发表日期: 2014
DOI: 10.1021/ci500080q
卷: 54, 期:6, 页:1700-1716
收录类别: SCI
英文摘要: Scoring functions are often applied in combination with molecular docking methods to predict ligand binding poses and ligand binding affinities or to identify active compounds through virtual screening. An objective benchmark for assessing the performance of current scoring functions is expected to provide practical guidance for the users to make smart choices among available methods. It can also elucidate the common weakness in current methods for future improvements. The primary goal of our comparative assessment of scoring functions (CASF) project is to provide a high-standard, publicly accessible benchmark of this type. Our latest study, i.e., CASF-2013, evaluated 20 popular scoring functions on an updated set of protein-ligand complexes. This data set was selected out of 8302 protein-ligand complexes recorded in the PDBbind database (version 2013) through a fairly complicated process. Sample selection was made by considering the quality of complex structures as well as binding data. Finally, qualified complexes were clustered by 90% similarity in protein sequences. Three representative complexes were chosen from each cluster to control sample redundancy. The final outcome, namely, the PDBbind core set (version 2013), consists of 195 protein ligand complexes in 65 clusters with binding constants spanning nearly 10 orders of magnitude. In this data set, 82% of the ligand molecules are "druglike" and 78% of the protein molecules are validated or potential drug targets. Correlation between binding constants and several key properties of ligands are discussed. Methods and results of the scoring function evaluation will be described in a companion work in this issue (doi: 10.1021/ci500081m).
语种: 英语
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内容类型: 期刊论文
URI标识: http://ir.sioc.ac.cn/handle/331003/38924
Appears in Collections:计算机化学与化学信息学研究室_期刊论文

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作者单位: 1.中科院上海有机化学研究所
2.澳门科技大学

Recommended Citation:
LI YAN,LIU ZHIHAI,LI JIE,et al. Comparative Assessment of Scoring Functions on an Updated Benchmark: 1. Compilation of the Test Set[J]. J. Chem Inf. Model.,2014,54(6):1700-1716.
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